Zinc in PDB 6u08: Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia

The structure of Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia, PDB code: 6u08 was solved by D.E.Bosch, M.M.H.De Moraes, J.D.Mougous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.60 / 2.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.760, 144.953, 64.186, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.8

The binding sites of Zinc atom in the Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia (pdb code 6u08). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia, PDB code: 6u08:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:0.0 occ:1.00 SG A:CYS1376 2.2 0.3 1.0 ND1 A:HIS1345 2.2 0.7 1.0 SG A:CYS1373 2.8 59.6 1.0 CE1 A:HIS1345 2.9 64.8 1.0 CG A:HIS1345 3.3 54.9 1.0 CB A:CYS1376 3.5 93.1 1.0 CB A:CYS1373 3.6 42.0 1.0 OE2 A:GLU1347 3.8 84.6 1.0 CB A:HIS1345 3.8 40.8 1.0 N A:CYS1373 3.9 42.8 1.0 CD A:GLU1347 3.9 74.7 1.0 NE2 A:HIS1345 4.1 64.1 1.0 CG A:GLU1347 4.2 62.1 1.0 CA A:CYS1373 4.2 49.7 1.0 N A:CYS1376 4.3 46.2 1.0 O A:HOH1603 4.3 52.1 1.0 CD2 A:HIS1345 4.3 53.3 1.0 OE1 A:GLU1347 4.3 74.2 1.0 CA A:CYS1376 4.5 53.4 1.0 O A:CYS1373 4.7 49.3 1.0 C A:CYS1373 4.8 48.9 1.0 CB A:ASN1342 4.8 48.5 1.0

Zinc binding site 2 out of 4 in the Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1501 b:0.9 occ:1.00 ND1 C:HIS1345 2.2 55.3 1.0 SG C:CYS1373 2.5 57.7 1.0 SG C:CYS1376 2.6 70.7 1.0 CE1 C:HIS1345 2.9 50.9 1.0 CG C:HIS1345 3.4 48.8 1.0 CB C:CYS1376 3.5 61.1 1.0 O C:HOH1606 3.5 55.6 1.0 CB C:CYS1373 3.5 46.9 1.0 N C:CYS1373 3.7 41.1 1.0 CB C:HIS1345 3.9 35.5 1.0 OE2 C:GLU1347 4.0 69.8 1.0 OE1 C:GLU1347 4.0 58.4 1.0 CA C:CYS1373 4.1 46.9 1.0 NE2 C:HIS1345 4.2 54.2 1.0 CD C:GLU1347 4.2 67.6 1.0 N C:CYS1376 4.3 44.1 1.0 CA C:CYS1376 4.4 50.3 1.0 CD2 C:HIS1345 4.4 46.6 1.0 O C:CYS1373 4.5 44.8 1.0 C C:CYS1373 4.6 51.7 1.0 C C:THR1372 4.8 47.0 1.0 CB C:ASN1342 4.9 46.0 1.0 CG2 C:THR1372 5.0 48.3 1.0

Zinc binding site 3 out of 4 in the Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1501 b:0.9 occ:1.00 ND1 E:HIS1345 2.2 65.5 1.0 SG E:CYS1376 2.4 75.4 1.0 SG E:CYS1373 2.7 56.5 1.0 CE1 E:HIS1345 2.9 57.5 1.0 CG E:HIS1345 3.3 53.8 1.0 CB E:CYS1376 3.4 66.4 1.0 CB E:CYS1373 3.8 47.0 1.0 CB E:HIS1345 3.9 39.4 1.0 NE2 E:HIS1345 4.0 55.8 1.0 N E:CYS1373 4.0 45.7 1.0 N E:CYS1376 4.0 45.1 1.0 OE2 E:GLU1347 4.1 80.0 1.0 CD2 E:HIS1345 4.2 53.7 1.0 OE1 E:GLU1347 4.3 68.0 1.0 CA E:CYS1376 4.3 59.2 1.0 CD E:GLU1347 4.3 74.1 1.0 CA E:CYS1373 4.3 49.5 1.0 CB E:ASN1342 4.4 51.9 1.0 O E:CYS1373 4.5 56.3 1.0 C E:CYS1373 4.7 50.4 1.0 CB E:PHE1375 4.8 54.8 1.0 C E:PHE1375 5.0 43.5 1.0

Zinc binding site 4 out of 4 in the Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Double-Stranded Dna-Specific Cytidine Deaminase Type VI Secretion System Effector and Cognate Immunity Complex From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1501 b:0.1 occ:1.00 SG G:CYS1376 2.4 73.6 1.0 SG G:CYS1373 2.6 61.9 1.0 N G:CYS1373 2.9 40.8 1.0 CB G:CYS1376 3.2 64.7 1.0 CB G:CYS1373 3.4 39.9 1.0 ND1 G:HIS1345 3.4 60.9 1.0 O G:HOH1611 3.4 53.4 1.0 CA G:CYS1373 3.6 45.0 1.0 OE2 G:GLU1347 3.6 82.9 1.0 OE1 G:GLU1347 3.7 73.7 1.0 CD G:GLU1347 3.8 73.7 1.0 C G:THR1372 3.9 44.4 1.0 O G:CYS1373 4.1 42.6 1.0 CE1 G:HIS1345 4.1 61.1 1.0 CA G:THR1372 4.2 40.7 1.0 CG2 G:THR1372 4.2 42.7 1.0 C G:CYS1373 4.2 42.5 1.0 N G:CYS1376 4.2 45.8 1.0 CA G:CYS1376 4.3 55.4 1.0 CG G:HIS1345 4.5 54.0 1.0 CB G:HIS1345 4.8 37.5 1.0 CB G:THR1372 4.8 46.2 1.0 CG G:GLU1347 4.9 68.8 1.0 O G:THR1372 5.0 44.2 1.0

B.Y.Mok, M.H.De Moraes, J.Zeng, D.E.Bosch, A.V.Kotrys, A.Raguram, F.Hsu, M.C.Radey, S.B.Peterson, V.K.Mootha, J.D.Mougous, D.R.Liu. A Bacterial Cytidine Deaminase Toxin Enables Crispr-Free Mitochondrial Base Editing. Nature V. 583 631 2020.
ISSN: ESSN 1476-4687
PubMed: 32641830
DOI: 10.1038/S41586-020-2477-4